The crystal structure of a DNA-binding protein, HucR, from Deinococcus radiodurans R1: a member of the MarR family of winged-helix transcriptional regulators

Abstract

The MarR family of transcriptional regulators is an important group of prokaryotic DNA binding proteins. As the family name implies, multiple antibiotic resistance, members of the MarR family often regulate the expression of resistance genes to multiple antibiotics, organic solvents, household disinfectants, detergents, and oxidative stress agents. Most MarR members act as transcriptional repressors and exist as homodimers in both free and DNA-bound states. DNA-binding is mediated via a winged-helix fold and is often relieved by anionic lipophilic ligands. Deinococcus radiodurans R1 was found to encode a 181 residue MarR homolog designated HucR (hypothetical uricase regulator). Biochemical evidence has shown that HucR negatively regulates expression of uricase and this repression is attenuated by the binding of uric acid, which is the natural substrate for uricase. In this study we present the crystal structure of HucR determined to 2.3 Å in the absence of ligand. In addition, a second crystal form of HucR was determined to 2.9 Å in which three dimers were observed in the asymmetric unit. Unlike the crystal structure of the MarR homolog, MexR, HucR does not display large conformational heterogeneity between dimers. Furthermore, superpositioning of the HucR dimer with the crystal structure of the OhrR dimer complexed with DNA suggests that HucR is in a "DNA ready" confirmation in which the lobes of the DNA binding domains are in a position compatible with DNA binding, with the exception of minor localized conformational changes needed at the amino termini of the recognition helices. This is in contrast to what is observed when comparing the crystal structures of the DNA-bound and unbound OhrR, in which there is a significant displacement of the DNA binding domains as a result of conformational changes that originate at the dimerization interface. The crystal structure of HucR in the absence of either ligand or DNA suggests that HucR is likely to be fixed in a "DNA ready" conformation. Thus, the crystal structure of HucR has given new insight into the MarR family of transcriptional regulators, proving that although these family members share similar structural folds, their mechanisms for transcriptional regulation are likely very specialized.